- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...Tags
* assigned: pjotrp
* type: enhancement
* status: in progress, halted
* priority: medium
* keywords: system, sheepdog
## Tasks
* [X] add locking functionality for tags - added borg with-lock...
- Letsencrypt
issue opened on Oct 13 2021 by Pjotr Prins, last updated on Jul 04 2023 by Pjotr Prins; 2 of 5 tasks done
...sheepdog_run.rb -c '/usr/bin/certbot renew --quiet' --always --tag CERTBOT >> ~/cron.log 2>&1
```
Add certificate
```
certbot certonly --nginx --agree-tos --preferred-challenges http -d ucscbrowser...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...that is streamed over the REST API - so people van validate client side (as a feature).
This mentions RDF - which I think
* aruni
was involved in. I (fredm) have tagged them here, for their evaluation...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...rm --cached --ignore-unmatch \
MouseTissuesRWWMay08.xls' --prune-empty --tag-name-filter cat -- --all
git reflog expire --expire=now --all && git gc --prune=now --aggressive
```
Note this rewrites...
- Add mouse data-set
issue opened on Jun 30 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi; 0 of 4 tasks done
...indexed by time. Also, we tag data by "animal.no." and "sex". So for a male version of "CC001" with animal number 1, we have "CC001_m_1". This is a problem---storing TS data---that Rob/Suheeta have...
- GN Markdown Editor Integration
issue opened on Jun 07 2024 by Alexander_Kabui, last updated on Aug 22 2024 by Alexander_Kabui; 9 of 10 tasks done
...Markdown Editor Integration
## Tags
* assigned: alexm
* status: in progress
* priority: high
* tags: markdown, integration, guile
## Notes
This is a to-do list to integrate the GN Markdown editor into...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
Variant Browser seems to be using mm9
## Tags
* assigned:
* priority: unclear
* type: bug
* status: stalled
* keywords: variant browser, mm9, from github
## Members
* acenteno
* robw
* pjotrp...
- Troubleshoot response inconsistencies for GN-llm
issue opened on Jan 10 2024 by Alexander_Kabui
...-llm
## Tags
* Assigned: Alex, SoloShelby
* Priority: High
* Type: LLM
* Keywords: LLM
* Status: In Progress
# Description
There are discrepancies when asking questions on Qnqa using Fahamu. Sometimes...
- Bug when a user quickly clicks "Compute" for mapping on the trait page
issue opened on Feb 06 2023 by Zachary Sloan, last updated on Feb 13 2023 by Zachary Sloan
...trait page
## Tags
* assigned: zsloan
* type: bug
* priority: high
* status: completed
* keywords: mapping, trait-page
## Description
The user sometimes gets a 405 error when they click the "Compute"...
- Temporary Traits Access Concerns
issue opened on Aug 03 2023 by Frederick Muriuki Muriithi
Temporary Traits Access Concerns
## Tags
* type: feature request
* priority: medium
* status: open
* assigned: fredm, zachs
* keywords: temp traits, temporary traits, access control
## Description...
- Tux01 hard disk crash
issue opened on Sep 29 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...One spinning disk crashed on Sept. 26th. It was used for Arthur's HOME and backups.
# Tags
* assigned: pjotrp
* priority: medium
* status: in progress
* keywords: system, tux01, hard disk crash
# Info...
- Clean Up
issue opened on Jan 02 2022 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
...Up
## Tags
* assigned: pjotrp, robw
* status: unclear
* priority: unclear
* type: database administration
* keywords: database, mariadb
## Description
Find all larger tables
```
SELECT TABLE_SCHEMA...
- ProbeSE
issue opened on Dec 30 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
ProbeSE
## Tags
* assigned: pjotrp
* status: unclear
* priority: medium
* type: enhancement
* keywords: database, mariadb, innodb, ProbeSE
## Description
Zach pointed out that ProbeSE is used on GN1...
- Support searching using SNP names
issue opened on Feb 15 2023 by Arun Isaac
...searching using SNP names
* tags: enhancement
SNPs are named in an rs### form (for example, rs429358).
=> https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism#Nomenclature
We should permit...
- StrainId wrong
issue opened on May 07 2024 by Pjotr Prins
...wrong
# Tags
* assigned: arthurc
* type: bug
* status: unknown
# Info
When I do:
```
MariaDB [db_webqtl]> SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id...
- Simplify `dataset.py` in GeneNetwork2
issue opened on Sep 13 2022 by Frederick Muriuki Muriithi
Simplify `dataset.py` in GeneNetwork2
## Tags
* assigned:
* priority: medium
* type: bug
* status: pending
* keywords: technical debt
## Description
The entire file
=>https://github.com/...
- Set Up gn-guile in tux02
issue opened on Aug 29 2024 by Munyoki Kilyungi, last updated on Oct 22 2024 by Munyoki Kilyungi; 3 of 3 tasks done
...Up gn-guile in tux02
## Tags
* assigned: bonfacem
* priority: high
* status: in-progress
* deadline: 2024-10-23 Wed
## Tasks
* [-] Create gn-guile container.
* [X] Merge gn2 UI PR.
=> https://github...
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
Search results presentation
## Tags
* assigned: alex
* status:in progress
* keywords: UI,search
## Notes
The idea is to research and find good design for search results in global search
Currently...
- Search results for SNP looks weird
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...looks weird
## Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: in progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395...
- Search Improvements: capital insensitive search for RIF+WIKI; Examples
issue opened on Mar 14 2023 by Arun Isaac, last updated on Aug 16 2024 by Munyoki Kilyungi
...Improvements: capital insensitive search for RIF+WIKI; Examples
## Tags
* assigned: bonfacem, rookie101
* priority: high
* type: ops
* keywords: virtuoso
## Description
RIF search is finally working...
- sample data caching bug
issue opened on Feb 11 2022 by Zachary Sloan, last updated on Mar 14 2023 by Arun Isaac
...few days (maybe later today).
The relevant caching code is here - https://github.com/genenetwork/genenetwork2/blob/2c22e593c59a9b4f9129a2e669443709d9c5154a/wqflask/base/data_set.py#L1288-L1317
# Tags...
- Set password when virtuoso containers are rebuilt
issue opened on Jul 07 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
...when virtuoso containers are rebuilt
## Tags
* assigned: bonfacem
* status: stalled
Whenever the virtuoso container is rebuilt, we manually have to reset the password. We should fix this by modifying...
- Report invalid search queries passed to the search API
issue opened on Feb 15 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
Report invalid search queries passed to the search API
* assigned: alex, arun
* tags: enhancement
* status: in progress
genenetwork2 offloads search to the genenetwork3 search API. When there is an...
- Replace Neo4J with Virtuoso
issue opened on Oct 22 2024 by Munyoki Kilyungi
Replace Neo4J with Virtuoso
## Tags
* assigned: bonfacem, soloshelby
* deadline: 2024-10-25 Fri
Currently, the RAG ingests TTL files into Neo4J. Replace this with Virtuoso.
- Gn3 network dependency
issue opened on Mar 18 2022 by Alexander Kabui, last updated on Jul 08 2022 by Alexander_Kabui; 0 of 2 tasks done
...while sending requests from gn3 from gn2
for tools like ctl and wgcna users run into network
errors if the gn3 server is down or other issues.Idea
is to use gn3 as library to avoid the above
## Tags...
- Remove References to Old gn-auth code
issue opened on Feb 21 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
Remove References to Old gn-auth code
## Tags
* assigned: bonfacem
* keywords: auth
* status: stalled
## Description
We still reference the old Racket gn-auth code. We should deprecate...
- Prevent Weak Passwords
issue opened on Feb 27 2024 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
Prevent Weak Passwords
## Tags
* status: open
* assigned: fredm
* priority: medium
* keywords: security, password, gn-auth
* type: feature-request, feature request
## Description
=> https://matrix...
- Pre-Cache Datasets
issue opened on Oct 24 2022 by Frederick Muriuki Muriithi
Pre-Cache Datasets
## Tags
* assigned:
* priority: medium
* type: enhancement
* status: open
* keywords: cache, optimisation
## Description
To improve the performance of the system when running...
- List of proposed changes for PCA traits/figures in Correlation Matrix page
issue opened on Jan 09 2023 by Zachary Sloan
...PCA traits/figures in Correlation Matrix page
## Tags
* type: feature, chore
* priority: medium
* assigned: zsloan
* status: in-progress
* keywords: pca, correlations
## Description
Rob proposed the...
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
Parsing genotyfiles
## Tags
* assigned: alexm
* type: debug
* priority: high
* status: in progress
## Once you identify the genofile identify
the file in the GENOTYPE_FILES and extract sample_listx...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Multi-trait heat map failed
## Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: stalled
* keywords: heatmap, from github
## Members
* zsloan
* pjotrp
* echesler
## Description...
- Move GN Racket Rest API to GNU Guile
issue opened on Jan 08 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
...Tags
* assigned: bonfacem
* priority: medium
* type: API, metadata
* keywords: API
* status: stalled
## Description
Currently, gene aliases retrieval relies on querying the outdated GN3 Rest Server...
- Missing Python Module(s) for GeneNetwork3
issue opened on Sep 19 2022 by Frederick Muriuki Muriithi
...Tags
* type: bug
* priority: high
* status: open
* keywords: python-modules
## Description
Missing modules when you try launching genenetwork3 locally:
* python-typing-extensions
The module needs...
- MGAMMA LMM
issue opened on Aug 19 2024 by Artyom Bologov; 3 of 5 tasks done
...LMM
MGamma does GWAS, which means it has to do Linear Mixed Models—both univariate and multivariate.
# Tags
* assigned: pjotrp, artyom
* type: feature
* priority: high
# Tasks
* [X] Kinship matrix...
- MGAMMA Convert
issue opened on Apr 17 2024 by Pjotr Prins, last updated on May 18 2024 by Artyom Bologov; 7 of 11 tasks done
MGAMMA Convert
MGamma can convert between different formats.
# Tags
* assigned: pjotrp, artyom
* type: feature
* priority: high
# Tasks
* [X] Store genotypes as floats instead of doubles in lmdb
* [X]...
- MGAMMA CLI
issue opened on Apr 17 2024 by Pjotr Prins, last updated on May 18 2024 by Artyom Bologov; 4 of 6 tasks done
...command line interface
# Tags
* assigned: pjotrp, artyom
* type: feature
* priority: high
# Tasks
* [ ] Provide sane CLI interface
* [X] Add --map-size 10M switch
* [X] Use lmdb files instead of dir...
- Zoomed mapping result are empty for certain traits
issue opened on Apr 11 2022 by Zachary Sloan, last updated on Apr 13 2022 by Zachary Sloan
...by clicking the top pink bar ("8x expanded WebQTL map") no points are displayed: https://genenetwork.org/show_trait?trait_id=NM_029911&dataset=UTHSC_BXD_WB_RNASeq1112
# Tags:
* source: robwwilliams...
- Make Partial Correlations Table Searchable
issue opened on Apr 22 2022 by Frederick Muriuki Muriithi
...Table Searchable
## Tags
* assigned: fredm
* priority: medium
* type: migration, feature-request
* status: pending
* keywords: partial correlations, datatables
## Description
@robw notes, correctly...
- Gn Markdown Editor implementation
issue opened on Aug 07 2023 by Alexander_Kabui, last updated on Sep 01 2025 by Alexander_Kabui; 5 of 5 tasks done
...to edit and live preview the results
also added to this is the ability to commit the changes directly to github repo:
Example of similar implementation
=> https://markdownlivepreview.com/
## Tags...
- Gn Markdown Editor implementation
issue opened on Nov 03 2023 by Alexander_Kabui; 4 of 5 tasks done
...git
## Tags
* assigned: alexm
* type: feature
* priority: high
## Tasks
* [x] implement initial apis;fetch page,edit and commit
* [x] UI: implement markdown page:editor
* [x] UI: add live preview...
- Handle "too-many-password-attempts"
issue opened on Feb 27 2024 by Frederick Muriuki Muriithi
Handle "too-many-password-attempts"
## Tags
* type: bug
* status: open
* assigned: fredm
* priority: medium
* keywords: security, password
## Description
=> https://matrix.to/#/!mBYtTotZGiPpHmjJnI...
- Planned Guix Updates
issue opened on Nov 14 2025 by Munyoki Kilyungi
Planned Guix Updates
## Tags
* status: open
* priority: medium
* type: enhancement
* assigned: fredm, bonfacem
* keywords: guix-bioinformatics, guix
* interested: pjotrp, aruni
## Description
The...
- Query Bug: DatabaseError
issue opened on Oct 27 2025 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
...DatabaseError
## Tags
* assigned: fredm, bonfacem
* priority: high
* status: open
* type: bug
* keywords: gnqna
## Descriptions
* Go to https://genenetwork.org/gnqna
* Type in a query
* Press "Enter"...
- GN-LLM Integration
issue opened on Dec 12 2023 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui; 3 of 3 tasks done
...com/ShelbySolomonDarnell/GN-LLMs) into Genenetwork as a search.
For reference on the initial implementation, please visit:
=> https://github.com/ShelbySolomonDarnell/GN-LLMs
## Tags
* Assigned: alexm...
- Rating System: No Indication for Login Requirement
issue opened on Jul 24 2024 by Solomon Shelby
Rating System: No Indication for Login Requirement
## Tags
* type: bug
* status: open
* priority: medium
* assigned: alex, shelby
* keywords: gnqna, user experience, UX
## Description
=> https://cd...
- Get GNQA Ready for evaluation
issue opened on Mar 21 2024 by Solomon Shelby, last updated on Jul 24 2024 by Solomon Shelby; 2 of 2 tasks done
...for evaluation
## Tags
* Assigned: alexm, shelbys
* Keywords: UI, GNQA, evaluation
* Type: immediate
* Status: completed
## Description
We need to publish a paper on GeneNetwork Question & Answering...
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
GN1 annotation page broken
## Tags
* assigned: zsloan, pjotrp
* priority: high
* status: overdue
* type: bug
* keywords: GN1, genenetwork1, annotation, from github
## Description
=> https://github...
- rewrite sampledata fetching with genofiles using scheme
issue opened on Jul 19 2023 by Alexander_Kabui, last updated on Sep 01 2025 by Alexander_Kabui; 2 of 6 tasks done
rewrite sampledata fetching with genofiles using scheme
## Tags
* assigned: alexm,
* type: improvement
* priority: high
* status: stalled, closed.
## Notes
having identified ways to link genofiles...
- Replace Redis with SQL
issue opened on Mar 12 2025 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
Replace Redis with SQL
## Tags
* status: open
* priority: low
* assigned: fredm
* type: feature, feature-request, feature request
* keywords: gn-uploader, uploader, redis, sqlite, sqlite3...
- "Delete All" Phenotypes Path Fails on Production.
issue opened 11 days ago by Frederick Muriuki Muriithi
...on Production.
## Tags
* assigned: fredm
* priority: medium
* keywords: gn-uploader, uploader, data, datasets
* status: open
* type: bug
## Description
The issue occurs in the background/asynchronous...
- Jobs: Allow Job Cascades
issue opened on Nov 05 2025 by Frederick Muriuki Muriithi
Jobs: Allow Job Cascades
## Tags
* status: open
* priority: medium
* type: enhancement
* assigned: fredm, zsloan
* keywords: gn-libs, genenetwork, async jobs, asynchronous jobs, background jobs...
- Synchronise gn-docs Changes
issue opened 4 weeks ago by Frederick Muriuki Muriithi, last updated 12 days ago by Johannes Medagbe
Synchronise gn-docs Changes
## Tags
* assigned: fredm
* interested: pjotrp, bonfacem
* status: open
* priority: high
* type: feature-request, feature request
* keywords: gn-guile, gn-docs...
- Rework Hard Dependence on Github
issue opened on Feb 14 2025 by Frederick Muriuki Muriithi, last updated on Feb 14 2025 by Frederick Muriuki Muriithi
Rework Hard Dependence on Github
## Tags
* status: open
* priority: medium
* type: bug
* assigned: alexm
* assigned: bonfacem
* assigned: fredm
* keywords: gn-guile, github
## Description
Currently...
- Rendering Images Linked in Markdown Documents
issue opened on Feb 11 2025 by Frederick Muriuki Muriithi
...Documents
## Tags
* status: open
* priority: high
* type: bug
* assigned: alexm, bonfacem, fredm
* keywords: gn-guile, images, markdown
## Description
Rendering images linked within markdown documents...
- New Privileges: Samples Ordering
issue opened on Sep 19 2024 by Frederick Muriuki Muriithi
New Privileges: Samples Ordering
## Tags
* status: open
* assigned: fredm
* interested: @zachs, @jnduli, @flisso
* priority: medium
* type: feature-request, feature request
* keywords: gn-auth, auth...
- Enable all DataTables to call the same code
issue opened on Jul 26 2022 by Zachary Sloan, last updated on Jul 27 2022 by Zachary Sloan
...same code
# Tags
* assigned: zsloan
* priority: medium
* type: refactor
* status: open, in progress
* keywords: tables, javascript
# Description
Currently most DataTables are drawn independently, so...
- Error Adding Trait(s) to Collection(s) While Logged Out
issue opened 6 weeks ago by Frederick Muriuki Muriithi, last updated 6 weeks ago by Johannes Medagbe
...(s) While Logged Out
## Tags
* type: bug
* status: open
* priority: high
* assigned: zachs, fredm
* keywords: gn2, genenetwork2, genenetwork 2, collections
## Description
### Steps to Reproduce
* Go to...
- GN1 symbols
issue opened on Nov 23 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi; 0 of 2 tasks done
...symbols
# Tags
* assigned: pjotrp, arthurc
* type: bug
* priority: medium
* status: unclear
* keywords: GN1, symbols
# Tasks
* [ ] fix font issue
* [ ] fix linked webqtl images
# Info
The fonts differ...
- GN1 Slowness
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...Tags
* assigned: ??
* type: bug
* priority: high
* keywords: GN1
## Description
GN1 needs to clean up the following
```
GNRoot="/gnshare/gn"
find $GNRoot/web/tmp -mmin +100 -exec rm -rfv...
- GN1 Production
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi; 3 of 8 tasks done
...for that.
## Tags
* type: bug
* priority: critical
* keywords: GN1
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs, robw
## List of outstanding issues
(see also E-mail Rob 14 Sep 2021)...
- Marker covariates implemented wrong in rqtl_wrapper.R
issue opened on Sep 22 2021 by Zachary Sloan, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...covariates in rqtl_wrapper.R is wrong. For the time being,
I've removed this option. Currently just waiting on Danny to get back to me with the fix (which I'll then add to rqtl_wrapper.R)
## Tags...
- Markdown docs
issue opened on Sep 10 2022 by Pjotr Prins
...garbage
> file that is about 10 years old. Love to update it.
> Is there a way to force line wraps at some practical length?
## Tags
* assigned: pjotrp, zsloan, robw, arthurc
* type: enhancement...
- Arthur mentioned last meet that GeneNetwork2 does not redirect http urls to https.
issue opened on Dec 05 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...org/
# nginx snippet
```
if ($scheme = http) {
return 301 https://$server_name$request_uri;
}
```
## Tags
* assigned: pjotr, arthur, jgart
* type: bug
* priority: medium
* status: unclear...
- guix-bioinformatics: Remove `guix-rust-past-crates` channel
issue opened on Oct 27 2025 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
...-past-crates` channel
## Tags
* assigned: alexm, bonfacem
* interested: fredm
* priority: normal
* status: open
* type: bug
* keywords: guix-bioinformatics, guix-rust-past-crates, guix, rust, crates...
- Document API endpoints for GeneNetwork3
issue opened on Mar 04 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...API endpoints for GeneNetwork3
Here's a simple way that SourceHut documents their API endpoints with markdown.
=> https://git.sr.ht/~sircmpwn/sr.ht-docs/tree/master/builds.sr.ht/api.md
## Tags...
- Add LICENSE page to GN2
issue opened on Dec 12 2022 by Pjotr Prins
...LICENSE page to GN2
GN1 has a nice license page
=> http://gn1.genenetwork.org/conditionsofUse.html
we should copy that on GN2.
## Tags
* assigned: zsloan, pjotrp
* priority: medium
* type: enhancement...
- LMM precomputed scores
issue opened on Mar 16 2023 by Pjotr Prins, last updated on May 07 2024 by Pjotr Prins; 0 of 1 tasks done
LMM precomputed scores
Here we will track introducing a new precomputation of scores for GN. Interestingly, this ties in with our xapian search and fast querying of value ranges.
# Tags...
- Scree Plot appears to be incorrect
issue opened on May 19 2022 by Zachary Sloan, last updated on Jun 15 2022 by BonfaceKilz
...are, it can be used to verify GN2's Scree Plot).
See
=> https://gist.github.com/sens/195214c1833d435b3406fa55abf2b6f4 Jupyter notebook
for a demo on what it should look like using the GN API.
## Tags...
- Fix Pairscan Mapping
issue opened on Jan 13 2025 by Alexander_Kabui
...Mapping
## Tags
* assigned: alexm,
* priority: medium,
* type: bug
* keywords: pairscan, debug, fix, mapping
## Description
Pairscan mapping is currently not working:
Error:
```
GeneNetwork 3.12-rc1...
- Fix Missing Genotype Files for GEMMA
issue opened on Sep 13 2022 by Frederick Muriuki Muriithi, last updated on Sep 20 2022 by Frederick Muriuki Muriithi; 1 of 3 tasks done
...Tags
* assigned:
* priority: medium
* type: bug
* status: pending
* keywords: gemma, technical debt
## Description
Run GEMMA (under "Mapping Tools") for
=> https://cd.genenetwork.org/show_trait...
- Correlations are not including f1 parents
issue opened on Nov 07 2022 by AlexanderKabui, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
...f1 parents
## Tags
* assigned:alexm,zsloan
* type:bug
* priority: high
* status:ongoing
* keywords: correlation,f1
## Description
Correlations should be including parents/F1s among the samples...
- Long samplenames overflow in Haplotype Analyst
issue opened on Nov 11 2022 by Zachary Sloan
Long samplenames overflow in Haplotype Analyst
## Tags
* priority: medium
* type: UI
* assigned: zsloan
* status: ongoing
* keywords: global search, phenotypes
## Description
For any BXD mapping...
- Fix Broken Global Search UI
issue opened on Jan 07 2025 by Alexander_Kabui, last updated on Jan 07 2025 by Alexander_Kabui; 0 of 2 tasks done
...Tags
* Assigned: alexm, zsloan
* Priority: high
* status: in progress
* Keyword : search, UI, bug, Refactor
* Type: UI, bug
## Description
The Global search UI layout is broken on certain browser...
- issues/fix-genotype-filename-HSNIH-Palmer.gmi
issue opened on Jun 27 2023 by GregFa
...filename HSNIH-Palmer
## Tags
* assigned: pjotrp
* type: bug fix
* priority: high
## Description
When using the Rest API to get the groups for "rat", it mentions the group HSNIH-Palmer.
But the REST...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
Fetch trait names for phenotypes
## Tags
* assigned:
* status: pending
* priority: unclear
* type: feature-request, enhancement
* keywords: phenotype, from github
## Members
* robw
* rupertoverall...
- Add Cis-Trans plot
issue opened on Apr 07 2023 by Pjotr Prins
Add Cis-Trans plot
After we complete precompute we should add Cis-Trans plots for eQTL datasets.
See also
=> ../../topics/systems/mariadb/precompute-mapping-input-data.gmi
# Tags
* assigned: zsloan...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
..."main" group
# Tags
* assigned: zsloan
* priority: medium
* type: feature-request
* status: open, in progress
* keywords: data, meta-data
# Description
Currently you can't do an analysis beween traits...
- Show Last Edited
issue opened on Jul 24 2023 by Frederick Muriuki Muriithi
Show Last Edited
## Tags
* type: feature request
* priority: medium
* assigned: fredm
* keywords: editing
* status: open
## Description
Following the GNSoC Plenary meeting of Thursday, 20 July 2023...
- Edit Dataset Metadata
issue opened on Jan 10 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi; 4 of 6 tasks done
...Tags
* assigned: bonfacem
* priority: high
* type: editing
* status: stalled
* keywords: metadata editing
## Description
Currently, we can only showcase dataset metadata. This task involves adding...
- Handle Configuration Files
issue opened on Dec 03 2021 by BonfaceKilz, last updated on Oct 12 2022 by Munyoki Kilyungi
...imports whenever we use blueprints. Unfortunately, a huge chunk of the code base uses "utility/tools.py" to get configuration settings; and removing this would make gn2 as is disfunctional.
# Tags...
- Decouple Tasks in Correlations Results Display
issue opened on Oct 24 2022 by Frederick Muriuki Muriithi, last updated on Nov 25 2022 by Frederick Muriuki Muriithi
Decouple Tasks in Correlations Results Display
## Tags
* type: bug
* priority: medium
* assigned: alexm
* keywords: correlations
* status: ongoing
## Description
=> https://github.com/...
- Database Migrations
issue opened on Oct 19 2022 by Frederick Muriuki Muriithi
...Tags
* assigned:
* type: feature
* priority: high
* keywords: database migrations
* status: pending
## Description
There might need to be some form of database migration to help keep the
* schema...
- Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel
issue opened on Sep 22 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...route is nasty and probably error prone. bcftools same, same. Arthur, if you copy the VCF files to tux01 and tell me when and where, I can have a go at setting up a tool chain we/you can use.
## Tags...
- Add the option to save traits uploaded with the Submit Trait option
issue opened on Jul 19 2022 by Zachary Sloan
...save traits uploaded with the Submit Trait option
# Tags
* assigned: zsloan
* priority: medium
* type: feature-request
* status: open, in progress
* keywords: data, meta-data
# Description
Current the...
- issues/custom_data_for_scatterplot.gmi
issue opened on Mar 09 2023 by Zachary Sloan
...Tags
* assigned: zsloan
* type: feature
* priority: high
* status: in-progress
* keywords: scatterplot, correlation
## Description
Currently the correlation scatterplot just takes the two trait/...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...commented out
## Tags
* assigned: zsloan
* priority: high
* type: bug
* status: unclear
* keywords: CSV, from github, meta data
## Description
=> https://github.com/genenetwork/genenetwork2/issues/594...
- Create Custom RIF XAPIAN Index
issue opened on Oct 16 2024 by Munyoki Kilyungi, last updated on Oct 22 2024 by Munyoki Kilyungi
...RIF XAPIAN Index
## Tags
* assigned: bonfacem
* priority: medium
* status: in-progress
* deadline: 2024-10-23 Wed
## Description
Given the GN Wiki search page:
=> https://cd.genenetwork.org/genewiki...
- Correlations: Fewer Results than Expected
issue opened on Nov 22 2022 by Frederick Muriuki Muriithi
...Fewer Results than Expected
## Tags
* type: bug
* priority: critical
* status: open
* assigned: zsloan, zachs
* keywords: correlations
## Description
Doing a search for top 500 covariates and get...
- Using guix-bioinformatics in a channels.scm file
issue opened on Aug 15 2021 by Efraim Flashner, last updated on Oct 09 2022 by Pjotr Prins
...we don't have a guix-bioinformatics git server that is *not* gitlab or github.
I think we should move to ssh keys and cgit. The latter has to run in a container, ideally.
## Tags
* assigned: efraimf...
- Guix: Using guix shell with root file
issue opened on Jan 27 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Tags
* assigned: jgart
* type: unclear
* status: unclear
* priority: low
* keywords: guix, guix shell, root file
## Description
```
guix shell --root
```
Let's benchmark and test these options to...
- Show Template for when Git URL is not Found
issue opened on Sep 28 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...not Found
## Tags
* type: bug
* assigned: jgart
* priority: medium
* keywords: binderlite, template
## Description
Let's add a template for when a url fails because the user entered the wrong
url or...
- Return canned text if notebook description returns none
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Return canned text if notebook description returns none
## Tags
* type: bug
* assigned: jgart
* priority: high
* status: in progress
* keywords: binderlite, notebooks
## Description
Notebooks that do...
- Add Regular Expression to Prevent Invalid Input
issue opened on Oct 01 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Add Regular Expression to Prevent Invalid Input
## Tags
* type: bug
* assigned: jgart
* status: unclear
* keywords: binderlite, notebooks
* priority: high
## Description
Add regex to the html form to...
- Add configuration to set server name
issue opened on Nov 10 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Tags
* assigned: jgart
* type: feature-request
* status: unclear
* priority: high
* keywords: binderlite, notebooks, configuration
## Description
Let's use environment variables as configuration...
- UI issues/improvements
issue opened on Jul 26 2023 by Zachary Sloan
.../improvements
## Tags
* assigned: fredm, zsloan
* priority: medium
* status: open
* keywords: authentication, authorisation, oauth2, resources, ui
* type: feature-request
## Description
Linking data...
- Paginate Resources Page
issue opened on Jul 27 2023 by Frederick Muriuki Muriithi
Paginate Resources Page
## Tags
* priority: medium
* status: open
* assigned: fredm, zachs
* keywords: resources, data linking, auth
* type: feature request
## Description
Some of the Resources have...
- Bug with linking data
issue opened on Jul 26 2023 by Zachary Sloan, last updated on Oct 19 2023 by Frederick Muriuki Muriithi
...with linking data
## Tags
* assigned: fredm, zsloan
* priority: high
* status: open
* keywords: authentication, authorisation, oauth2, xapian
* type: bug
## Description
While trying to link some newly-...
- Various UI issues raised by Rob (8/19/2024)
issue opened on Aug 19 2024 by Zachary Sloan, last updated on Sep 18 2024 by Zachary Sloan; 12 of 13 tasks done
...raised by Rob (8/19/2024)
# Tags
* assigned: zsloan
* keywords: user-interface
* priority: medium
* open
## Tasks
* [X] Fix collection encoding issue
* [X] Don't import empty collections (like the...
- Add Case Attributes to RDF
issue opened on Sep 03 2024 by Munyoki Kilyungi
Add Case Attributes to RDF
## Tags
* assigned: bonfacem
* priority: high
* status: open
## Description
Add case attributes and their metadata into RDF.
- Add search, select and export to datatables table
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Add search, select and export to datatables table
## Tags
* assigned: bonfacem, zsloan
* priority: low
* type: feature-request
* status: unclear
* keywords: datatables, UI, low...
- issues/add-pluto-notebooks.gmi
issue opened on Jun 27 2023 by GregFa
...Pluto Notebooks
## Tags
* assigned: pjotrp
* type: feature
* priority: high
## Description
Host Pluto Notebooks in GeneNetwork. As a proof of concept, we host:
=> https://notebooks.one/ notebooks.one...
- Add option to directly link to mapping results
issue opened on Jan 19 2023 by Zachary Sloan
Add option to directly link to mapping results
## Tags
* assigned: zsloan
* keywords: mapping
* priority: medium
## Description
Currently it's not possible to link to mapping results, so I'm adding a...
- Add genotype file paths to RDF
issue opened on Jun 19 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
...RDF
## Tags
* assigned: bonfacem
* type: bug
* status: stalled
In Penguin2, genotype files are located in: /export/data/genenetwork/genotype_files/genotype. Each genotype files has an identifier to a...
- Speed Up QC on R/qtl2 Bundles
issue opened on Jun 24 2024 by Frederick Muriuki Muriithi
.../qtl2 Bundles
## Tags
## Description
The default format for the CSV files in a R/qtl2 bundle is:
```
matrix of individuals Ă— (markers/phenotypes/covariates/phenotype covariates/etc.)
```
(A) (f/F)ile...
- Database: `ProbeSetSE` Schema Bug
issue opened on Mar 22 2024 by Frederick Muriuki Muriithi, last updated on Mar 22 2024 by Frederick Muriuki Muriithi
...Schema Bug
## Tags
* type: bug
* priority: critical
* status: open
* keywords: database, mariadb, schema
* assigned:
## Description
The schemas are defined as follows:
```
MariaDB [db_webqtl]> DESC...
- When binderlite finds an unkown package in a guix manifest
issue opened on Oct 01 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...be managed by the sysadmin only for security reasons?
It's probably a security risk since a guix channel can pull in arbitrary
packaged code that might not be audited or fully trusted.
## Tags...
- Penguin2 RAID 5
issue opened on Feb 28 2025 by Pjotr Prins
...5
# Tags
* assigned: @fredm, @pjotrp
* status: in progress
# Description
The current RAID contains 3 disks:
```
root@penguin2:~# cat /proc/mdstat
md0 : active raid5 sdb1[1] sda1[0] sdg1[4]
/dev/md0...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...genomes. Here we track a next generation annotation system which will support versions of annotation with a matching reference genome. In the future we'll build this out with pangenome support.
# Tags...
- Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
issue opened on Jul 21 2022 by Zachary Sloan, last updated on Sep 14 2022 by Pjotr Prins
Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
# Tags
* assigned: zsloan
* priority: medium
* type: feature-request
* status: open, in progress...
- Broken Collections Features
issue opened on Apr 07 2025 by Frederick Muriuki Muriithi, last updated on Apr 08 2025 by Frederick Muriuki Muriithi
...Collections Features
## Tags
* type: bug
* status: open
* priority: high
* assigned: zachs, fredm
* keywords: gn2, genenetwork2, genenetwork 2, collections
## Descriptions
There are some features in...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Error when attempt to zoom to a chromosome after mapping a PCA trait
## Tags
* assigned: zsloan
* type: bug
* priority: high
* status: unclear
* keywords: PCA, from github, high...
- Adding principal component to collection returns an error
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Alexander Kabui
Adding principal component to collection returns an error
## Tags
* assigned: alex
* status: unclear
* priority: high
* type: bug
* keywords: collections, from github
## Members
* rupertoverall...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
AI UI Enhancements
## Tags
* Assigned: alexm, shelbys
* Keywords: UI, GNQA
* Type: critical
* Status: In Progress
## Description
This issue addresses user feedback received during the testing phase...
- Octopus sysmaintenance
issue opened on Oct 12 2021 by Pjotr Prins, last updated on Dec 12 2025 by Pjotr Prins; 1 of 8 tasks done
...all nodes. We also need to work on user management and network storage.
See also
=> ../../topics/systemtopics/systems/hpcs/hpc/octopus-maintenance
# Tags
* assigned: pjotrp, efraimf, erikg, andreag...
- GN2 Integration with LLM search using cached results
issue opened on Aug 26 2024 by John Nduli, last updated on Sep 09 2024 by Alexander_Kabui; 2 of 6 tasks done
...using cached results
## Tags
* assigned: jnduli, alexm, bmunyoki
* keywords: llm, genenetwork2
* type: enhancement
* status: open
## Description
We'd like to include LLM searches integrated into our...
- Logging Handler Improvements for GN3
issue opened on Jun 11 2024 by John Nduli
...Handler Improvements for GN3
## Tags
* assigned: jnduli
* priority: low
* type: enhancement
## Goal
Our logs help us fix problems without the need for LOG_LEVEL=DEBUG
## Background
When fixing logs in...
- CLI Script to Generate Text Files
issue opened on Dec 19 2022 by Frederick Muriuki Muriithi, last updated on Jan 23 2023 by Alexander_Kabui
...Tags
* assigned: alexm
* type: feature, improvement
* priority: high
* keywords: correlations, materialised views, optimisation, script
* status: inprogress
## Description
This issue supercedes the...
- CTL Maps Error
issue opened on Apr 08 2025 by Frederick Muriuki Muriithi, last updated on Apr 08 2025 by Frederick Muriuki Muriithi
CTL Maps Error
## Tags
* type: bug
* status: open
* priority: high
* assigned: alexm, zachs, fredm
* keywords: CTL, CTL Maps, gn3, genetwork3, genenetwork 3
## Description
Trying to run the CTL Maps...
- Cool Interfaces We Should Emulate
issue opened on Apr 13 2022 by BonfaceKilz, last updated on Apr 14 2022 by BonfaceKilz
Cool Interfaces We Should Emulate
## Tags
* assigned: bonfacem, zachs, robw
* type: ui
* status: stalled
* priority: low
* keywords: ui
## Description
[From RW]
We have talked about upgrading our...
- Check for Mandatory Settings
issue opened on Oct 18 2024 by Frederick Muriuki Muriithi; 0 of 3 tasks done
...Tags
* status: open
* priority: high
* type: bug, improvement
* interested: fredm, bonz
* assigned: jnduli, rookie101
* keywords: GN3, gn3, genenetwork3, settings, config, configs, configurations...
- Generate Heatmaps Failing
issue opened on Oct 15 2024 by Frederick Muriuki Muriithi, last updated on Apr 08 2025 by Frederick Muriuki Muriithi
Generate Heatmaps Failing
## Tags
* type: bug
* status: open
* priority: medium
* assigned: fredm, zachs, zsloan
* keywords: genenetwork3, gn3, GN3, heatmaps
## Reproduce
* Go to...
- Decommission machines
issue opened on Oct 06 2021 by Pjotr Prins, last updated on Sep 22 2023 by Pjotr Prins; 11 of 22 tasks done
...machines
# Tags
* assigned: pjotrp, arthurc, dana
* priority: high
* keywords: systems
* type: system administration
* status: unclear
# Tasks
## Running (OK)
* rabbit is used for backups (R815 - 2010...
- Brittle Fix for Editing Metadata
issue opened on Aug 02 2023 by Frederick Muriuki Muriithi
Brittle Fix for Editing Metadata
## Tags
* type: bug
* priority: high
* assigned: fredm, zachs, bonz
* keywords: metadata, editing
* status: open
## Description
=> https://github.com/...
- Each shepherd service needs its own guix profile.
issue opened on Nov 03 2021 by Efraim Flashner, last updated on Jun 21 2024 by Pjotr Prins
...guix binary, acting like a time machine. It is
used to fire up a guix shell/environment:
* bnw
* cronjob-gitea
* cronjob-pubmed (genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags...
- Tasks
issue opened on Jun 27 2023 by GregFa, last updated on Apr 26 2024 by Pjotr Prins; 0 of 2 tasks done
...integration
## Tags
* assigned: pjotrp, zachs
* type: feature
* priority: high
## Description
Integrate BulkLMM in GeneNetwork. The first step is to test the command line interface to BulkLMM in...
- Tux02 Production
issue opened on Oct 07 2021 by Pjotr Prins, last updated on Jun 13 2025 by Pjotr Prins; 17 of 22 tasks done
...staging machine. This machine is aimed to be rock solid. The idea is to have 4-6 times a year upgrades. Also we should be able to roll back on an upgrade and be able to create time machines.
## Tags...
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...up parallel page server
* + [ ] Handle headers and footers
* + [ ] Create portal page
* + [ ] Show specific datasets
* + [ ] Show specific publications
* + [ ] Show specific twitter feed
# Tags...
- gn-guile Configurations
issue opened on Nov 18 2024 by Frederick Muriuki Muriithi; 1 of 1 tasks done
...-guile Configurations
## Tags
* type: bug
* assigned:
* priority: high
* status: open
* keywords: gn-guile, markdown editing
* interested: alexk, bonfacem, fredm, pjotrp
## Description
=> https://git...
- Databases Getting Out of Wack
issue opened on Mar 03 2022 by jgart, last updated on Mar 16 2023 by Pjotr Prins
...reaper module that runs as a script:
=> https://github.com/genenetwork/genenetwork2/blob/testing/scripts/maintenance/QTL_Reaper_v6.py
We'll create a new issue:
=> lmm-precomputed-scores.gmi
## Tags...
- Rebooting the GN production machine(s)
issue opened on Jan 01 2022 by Pjotr Prins, last updated on Oct 06 2022 by Pjotr Prins; 4 of 4 tasks done
...-module-crashes-on-14G-servers/td-p/6031769
The Linux kernel shows some fixes that are not on Tux01 yet
=> https://lkml.org/lkml/2021/2/17/970
In our case a simple reboot worked, fortunately.
## Tags...
- Implement Upload of Genotypes
issue opened 11 days ago by Frederick Muriuki Muriithi
Implement Upload of Genotypes
## Tags
* assigned: fredm
* priority: medium
* keywords: gn-uploader, uploader, data, datasets, genotypes
* status: open
* type: feature request, feature-request...
- Some correlations running very slowly
issue opened on Mar 06 2023 by Zachary Sloan, last updated on Mar 07 2023 by Pjotr Prins
...very slowly
## Tags
* assigned: zsloan, pjotrp
* type: bug
* priority: high
* status: in-progress
* keywords: correlations, database
## Description
Some correlations (it specifically seems to be ones...
- ProbeData
issue opened on Dec 30 2021 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac
ProbeData
## Tags
* assigned: pjotrp
* status: unclear
* priority: medium
* type: enhancement
* keywords: database, mariadb, innodb, ProbeData
## Description
Probe level data is used to examine the...
- CD is slow
issue opened on Jul 20 2025 by Pjotr Prins, last updated on Jul 24 2025 by Pjotr Prins; 2 of 8 tasks done
...Consortium M430v2 (Jun06) PDNN 1457545_at 9530036O11Rik long non-coding RNA, expressed sequence tag (EST) AK035474 with high bladder expression antisense EST 14 Kb upstream of Shh...
- GN1 Time machines
issue opened on Oct 07 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
...sudo 33730812 Wed, 2017-04-12 17:06:40 export/backup/artemis/mysql/gn_db_20180228/Geno.MYD
```
so you can see all the different versions. The matching code bases should be there too.
## Tags...
- Slow query
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Slow query
## Tags
* assigned: Uditgulati
* priority: high
* status: stalled
* keywords: slow query, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/419...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Tags
* type: bug
* priority: high
* keywords: GN1, Network Graph
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs
## Tracking
To reproduce this bug: select a 'shopping basket' and...
- Feature Request: Create Test Accounts
issue opened on Sep 16 2024 by Frederick Muriuki Muriithi, last updated on Sep 17 2024 by Frederick Muriuki Muriithi
...Accounts
## Tags
* assigned: fredm, alex
* status: open
* type: feature request, feature-request
* priority: medium
* keywords: gn-auth, auth, test accounts
## Description
From the requests on Matrix...
- Linking genotype files to datasets
issue opened on Jul 07 2023 by Alexander_Kabui, last updated on Jul 11 2023 by Alexander_Kabui
Linking genotype files to datasets
## Tags
* assigned: alexm
* type: debug
* priority: high
* status: in progress
## Notes
A dataset can have multiple groups. In order to fetch all possible sample...
- Correlation results wrong for certain traits/datasets
issue opened on Dec 12 2022 by Zachary Sloan, last updated on Dec 22 2022 by Zachary Sloan
...wrong for certain traits/datasets
## Tags
* assigned: alexm, zsloan, fredm
* priority: high
* status: ongoing
* keywords: correlations
## Description
(Note that this uses the update to using GN! text...
- Correlations: Returning Fewer Results
issue opened on Nov 07 2022 by AlexanderKabui, last updated on Nov 25 2022 by Zachary Sloan
...Returning Fewer Results
## Tags
* assigned: alexm
* priority: high
* status: ongoing
* keywords: correlations,fewer results
## Description
in some cases correlaton return fewer number of results
than...
- GN1 metadata
issue opened on Dec 09 2022 by Pjotr Prins; 0 of 3 tasks done
...it shows a missing PHP.
The problem can be replitated by logging into GN1 and selecting a dataset. Hit the info button and 'edit' next.
## Tags
* assigned: pjotrp
* priority: high
* status: overdue...
- Genewiki conversion
issue opened on Aug 26 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 0 of 3 tasks done
...in that repository and (2) create a rendered page that is found through
=> https://genenetwork.org/doc/genes/BRCA2
with an edit button, similar to
=> http://genenetwork.org/facilities/
## Tags...
- Fallbacks and backups
issue opened on Aug 31 2021 by Pjotr Prins, last updated on Jun 28 2024 by Pjotr Prins; 3 of 25 tasks done
...sheepdog server we may give it a DNS entry as sheepdog.genenetwork.org.
=> http://sheepdog.genenetwork.org/sheepdog/index.html
See also
=> /topics/systems/restore-backups Restore Backups
## Tags...
- Dump sample data to LMDB
issue opened on Dec 15 2022 by Munyoki Kilyungi, last updated on Mar 06 2024 by Munyoki Kilyungi; 0 of 5 tasks done
...probesets
* [ ] genotypes
* [ ] GN2/3 Integration
For RDF:
https://issues.genenetwork.org/search?query=assigned%3ABonfaceKilz+AND+tag%3Ain-progress+AND+priority%3Ahigh+AND+is%3Aopen&type=open-...
- Uploading Samples
issue opened on Sep 18 2024 by Frederick Muriuki Muriithi, last updated on Sep 19 2024 by Frederick Muriuki Muriithi
Uploading Samples
## Tags
* status: open
* assigned: fredm
* interested: acenteno, zachs, flisso
* priority: high
* type: feature-request
* keywords: gn-uploader, uploader, samples, strains...
- Implement File-Based, and CLI-Based Configuration for "gn-guile"
issue opened 9 days ago by Frederick Muriuki Muriithi, last updated 9 days ago by Frederick Muriuki Muriithi
...-guile"
## Tags
* type: feature
* assigned: fredm
* priority: high
* status: open (awaiting patch(es) review)
* keywords: gn-guile, config, configs, configuration
* interested: alexk, bonfacem, fredm...
- Investigate and Fix `rm` Command in `rqtl` Logs
issue opened on Jan 08 2025 by Alexander_Kabui, last updated on Jan 09 2025 by Munyoki Kilyungi; 4 of 6 tasks done
Investigate and Fix `rm` Command in `rqtl` Logs
## Tags
* assigned: alex, bonfacem
* type: Bug
* status: in progress
* keywords: external, qtl, rqtl, bug, logs
## Description
For QTL analysis...
- UM-HET3 Timing: Slow
issue opened on Oct 26 2024 by Frederick Muriuki Muriithi, last updated on Oct 26 2024 by Frederick Muriuki Muriithi
UM-HET3 Timing: Slow
## Tags
* type: bug
* status: open
* assigned: fredm
* priority: critical
* interested: fredm, pjotrp, zsloan
* keywords: production, container, tux04, UM-HET3
## Description
In...
- Improve Authorization Checks
issue opened 6 weeks ago by Frederick Muriuki Muriithi, last updated 6 weeks ago by Johannes Medagbe; 2 of 11 tasks done
Improve Authorization Checks
## Tags
* type: improvement, refactor
* assigned: fredm
* interested: zachs, bonfacem
* keywords: gn-auth, auth, authorisation, authorization
* priority: high...
- Investigate and fix "qtl2::calc_genoprob()" run due to failing with negative length vectors
issue opened 3 weeks ago by Lisso_, last updated 12 days ago by Johannes Medagbe
...failing with negative length vectors
## Tags
* Assigned: Flisso
* type: bug
* status: in progress
* interested: alexm
* key words: cross, qtl2, calc_genoprob, bugs
## Description
Running subset of...
- Migrate Genenetwork Production from tux03 to tux04, Jan2026-Feb2026
issue opened 9 weeks ago by Frederick Muriuki Muriithi, last updated 7 weeks ago by Frederick Muriuki Muriithi; 8 of 8 tasks done
...tux03 to tux04, Jan2026-Feb2026
## Tags
* assigned: fredm
* status: open
* priority: high
* type: migration
* keywords: migration, genenetwork, production
## Description
We need to migrate back to...
- Export Uploaded Data to LMDB and RDF Stores
issue opened on Nov 03 2023 by Frederick Muriuki Muriithi, last updated on Oct 20 2025 by Frederick Muriuki Muriithi; 0 of 6 tasks done
...Tags
* assigned: fredm, bonz
* priority: medium
* type: feature-request
* status: open
* keywords: API, data upload, gn-uploader
## Description
With the QC/Data Upload project nearing completion...
- GN1 annotation page broken
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Dec 17 2022 by Pjotr Prins; 0 of 2 tasks done
...page broken
## Tags
* assigned: zsloan, pjotrp
* priority: high
* status: testing
* type: bug
* keywords: GN1, genenetwork1, annotation, from github
## Tasks
* [ ] Fix PHP view
* [ ] Fix CKEDITOR...
- R Kernel Dying
issue opened on Jan 17 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Dying
## Tags
* assigned: jgart
* type: bug
* priority: high
* status: unclear
* keywords: R
## Core Dump
```
[I 08:45:24.502 NotebookApp] Writing notebook-signing key to /home/jgart/.local/share/...
- Build an AI system for GN
issue opened 7 weeks ago by Johannes Medagbe; 4 of 6 tasks done
...TAG(48:3)_HFD, is part of the EPFL LISP3 Study. It's a measurement of Liver Lipidomics: TAG48:3_HFD, which has side chain FA composition [TG12:0_18:1_18:2,TG14:0_16:0_18:3,TG14:0_16:1_18:2,TG14:0_16...
- Fetch trait data using genofiles
issue opened on Jul 11 2023 by Alexander_Kabui, last updated on Jul 13 2023 by Alexander_Kabui; 2 of 3 tasks done
Fetch trait data using genofiles
## Tags
* assigned:alexm,
* type:improvement
* priority: high
* status: in progress
## Notes
since Genenetwork database does not have all genotype files when fetching...
- Large datasets crash gemma
issue opened on Mar 12 2022 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi; 0 of 7 tasks done
...find that message). Or it may be GEMMA simply runs out of RAM and the kernel is busy cleaning up using the OOM reaper. See
=> https://lkml.iu.edu/hypermail/linux/kernel/2003.2/01012.html
## Tags...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 8 weeks ago by Pjotr Prins; 33 of 74 tasks done
Apps
GeneNetwork.org retains a number of apps. Currently they are managed by shepherd as `guix shell` services, but we should really move them to system containers.
# Tags
* assigned: pjotrp...
- Slow query
issue opened on May 27 2023 by Pjotr Prins, last updated on May 29 2023 by Pjotr Prins; 0 of 2 tasks done
...utf8mb4. When comparing text fields mariadb can't optimize because it is translating utf8mb3 for every comparison. Changing the table and indices to utf8mb4 or latin1 (on production) fixed it.
# Tags...
- Multivariate GEMMA hangs (issue 243)
issue opened on Aug 16 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...hangs (issue 243)
## Tags
* assigned: ??
* type: failure
* keywords: GEMMA
* status: unclear
* priority: high
## Description
=> https://github.com/genetics-statistics/GEMMA/issues/243
The simulated...
- Fallback issues
issue opened on Mar 22 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins; 3 of 6 tasks done
...also I created my own development VM in just an hour, so I don't have to mess with the fallback while others are using it.
# Tags
* type: bug
* assigned: pjotrp
* keywords: systems, fallback, deploy...
- GN2 Time Machines
issue opened on Aug 19 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 4 of 10 tasks done
...complexity has increased a lot because of interacting services and a larger dependency graph.
Here I track what it takes today to install a fallback instance of GN2 that is 'frozen' in time.
## Tags...
- Broken Aliases
issue opened on Oct 21 2024 by Frederick Muriuki Muriithi, last updated on Aug 15 2025 by Frederick Muriuki Muriithi; 3 of 4 tasks done
Broken Aliases
## Tags
* type: bug
* status: open
* priority: high
* assigned: pjotrp
* interested: pjotrp
* keywords: aliases, aliases server
## Tasks
* [X] Rewrite server in gn-guile
* [X] Fix menu...
- ProbeSetData
issue opened on Dec 31 2021 by Pjotr Prins, last updated on Mar 13 2023 by Pjotr Prins; 15 of 17 tasks done
...the ProbeSetData table and indices. At the end we have reduced the size by 25% and decided to keep the myisam format for this single table. In the future it may be replaced by lmdb or similar.
## Tags...
- ProbeSetXRef
issue opened on Dec 29 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
...Tags
* keywords: ProbeSetXRef, database, mariadb, innodb
* type: enhancement, documentation
* assigned: pjotrp
* status: unclear
* priority: medium
## Table ProbeSetXRef
Juggling indexes and...
- Hanging database
issue opened on Dec 21 2021 by Pjotr Prins, last updated on Mar 11 2023 by Pjotr Prins
...myisam to InnodB is the solution because it prevents full table locking.
Also it is better to use mydumper, mydumper locks MyISAM tables and does not lock InnoDB so the dump is consistent.
## Tags...
- Tux04/Tux05 disk issues
issue opened on May 03 2024 by Pjotr Prins, last updated on Sep 13 2025 by Pjotr Prins; 12 of 12 tasks done
...Tags
* assigned: pjotrp, aruni
* type: systems
* keywords: hardware
* status: unclear
* priority: medium
# Info
```
journalctl |grep mega
May 01 01:40:45 tux04 smartd[2440]: Device: /dev/bus/0...
- Speeding up GEMMA
issue opened on Nov 11 2025 by Pjotr Prins, last updated on Dec 12 2025 by Pjotr Prins; 5 of 15 tasks done
...a new build system and testing framework. In parallel we'll try to scale out on HPC using Arun's ravanan software.
There is no such thing as a free lunch. So, let's dive in.
# Description
# Tags...
- MariaDB: Move to InnoDB Engine
issue opened on Dec 28 2021 by Pjotr Prins, last updated on Apr 24 2024 by Pjotr Prins; 0 of 8 tasks done
...every table
* [ ] Check for primary key
* [ ] Check fulltext fields (see below)
* [ ] Convert to innodb
* [ ] Convert to utf8mb4 and utf8mb4_general_ci
## Tags
* assigned: pjotr
* type: enhancement...